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- PDB-5bph: Crystal structure of AMP complexed D-alanine-D-alanine ligase(DDL... -

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Basic information

Entry
Database: PDB / ID: 5bph
TitleCrystal structure of AMP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / D-alanine-D-alanine ligase (DDL) / drug target / bacterial cell wall synthesis
Function / homology
Function and homology information


D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosol
Similarity search - Function
D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain ...D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsTran, H.T. / Kang, L.W. / Hong, M.K.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
Authors: Tran, H.T. / Hong, M.K. / Ngo, H.P. / Huynh, K.H. / Ahn, Y.J. / Wang, Z. / Kang, L.W.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,22226
Polymers132,7194
Non-polymers2,50322
Water13,151730
1
A: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,66814
Polymers66,3602
Non-polymers1,30912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanine--D-alanine ligase
C: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,55312
Polymers66,3602
Non-polymers1,19410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.585, 106.071, 210.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
D-alanine--D-alanine ligase / D-Ala-D-Ala ligase / D-alanylalanine synthetase


Mass: 33179.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ddl, ddlB, YPO0557, y3624, YP_3627 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZIE7, D-alanine-D-alanine ligase

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Non-polymers , 5 types, 752 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.33 % / Description: Orthorhombic shaped crystal
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M sodium acetate, 0.1 M Bis-Tris pH 7.0, 29% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2013
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / % possible obs: 99.9 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.07 / Net I/av σ(I): 4.7 / Net I/σ(I): 50

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.7→34.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.019 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20949 7688 5 %RANDOM
Rwork0.17702 ---
obs0.17868 145553 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.533 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9296 0 163 730 10189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0199654
X-RAY DIFFRACTIONr_bond_other_d0.0010.029205
X-RAY DIFFRACTIONr_angle_refined_deg2.1791.99713067
X-RAY DIFFRACTIONr_angle_other_deg0.942321233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28551214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58625.013391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.411151598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4161536
X-RAY DIFFRACTIONr_chiral_restr0.130.21491
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02110822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022046
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8162.7454880
X-RAY DIFFRACTIONr_mcbond_other2.8142.7454877
X-RAY DIFFRACTIONr_mcangle_it3.7134.1066082
X-RAY DIFFRACTIONr_mcangle_other3.7134.1066083
X-RAY DIFFRACTIONr_scbond_it4.2893.2714774
X-RAY DIFFRACTIONr_scbond_other4.2883.2714775
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2524.7246986
X-RAY DIFFRACTIONr_long_range_B_refined7.74423.64911265
X-RAY DIFFRACTIONr_long_range_B_other7.74423.59411216
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.703→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 522 -
Rwork0.256 10221 -
obs--96.02 %

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